Engineered Protein 'Evolution' Proves Biological Complexity

by
Jeffrey P. Tomkins, Ph.D. *

Researchers recently announced the first systematic laboratory-induced mutation of successive amino acids in a nearly complete simple bacterial protein.1 The results demonstrated how protein chemistry and structure, in even the most simple of life’s proteins, are irreducibly complex. The research also showed how the random processes ascribed to genetic mutations are unable to propel favorable evolutionary progress that could lead to new selectable traits.

Proteins are chains of amino acids that are coded by the information contained in DNA. Three successive nucleotide bases of DNA code for a single amino acid of a protein, and cells use 20 different amino acids. The specific order of amino acids is required, not only for basic protein functionality, but also for optimized functionality.

In this study, researchers successively changed the DNA code of a bacterial gene to individually mutate every amino acid in a simple bacterial protein of 83 amino acids in length. They then tested the ability of that protein to interact with its target chemical—a ligand, which is a binding molecule in the cell. The section of protein that interacts with a ligand is called the “active site.” The researchers also tested the ability of successively mutated amino acids in the active site of the protein to bind to an artificial substrate.

The researchers ultimately proved that proteins have a variety of specific regions or sectors that are highly sensitive to mutation, meaning that amino acid changes in these regions are not tolerated and completely destroy protein function. They also demonstrated that proteins have other regions that are more tolerant of mutation, areas in which changes do not completely destroy the function of the protein. Instead, these changes reduce the protein’s optimization and lower its efficiency.

Virtually all amino acids in proteins play some specific role because proteins are not just linear chains of molecules—each has a specific chemical function. After they are formed, proteins are folded into specific three-dimensional structures. The linear order of amino acids determines the ability to be folded into specific functionally relevant shapes.

In the simple bacterial protein the researchers tested, 20 out of the 83 amino acids (24 percent) were highly intolerant of change, meaning that they are essentially off-limits to “random mutational evolutionary processes.” Many of these mutation-resistant amino acids were in key sectors of the protein associated with its interactive capabilities with its ligand binding partner. Unfortunately for evolutionary concepts, this is exactly where you would want mutations to occur if they were to aid new cellular interactions that might somehow produce a new trait.

The researchers successfully mutated an amino acid in the sector where the binding region was located, and they were able to get the protein to bind to a non-native ligand. In other words, they engineered the protein to bind to an unnatural lab chemical. This is something a protein would never have encountered in its natural bacterial cell environment. While this was a classic case of human-guided bioengineering in a high-tech laboratory environment, it was hardly an example of naturalistic evolution in a real cell or organism. Nevertheless, evolutionists proclaimed this as some sort of proof that proteins are able to evolve and find new binding partners.

While the other 63 amino acids in the protein could be changed successively and independently of each other without completely destroying the protein’s function, their changes were limited to only a few of the possible 19 other amino acids that they could be changed to—amino acids with similar chemistries. This is because many amino acid changes, even outside the most critical sectors, alter the overall chemistry and the three-dimensional properties of the protein in negative ways that lower the protein’s optimum functionality. It was also apparent that amino acids in different parts of the protein had irreducibly complex, long-range interactions with each other that also contributed to the proper function of the protein. These long-range interactions could only be engaged and accounted for after the protein was in its three-dimensional conformation.

Some evolutionary biologists claimed that this study showed how amino acids could change (mutate) and not destroy a protein’s function during that process of change, illustrating how molecular evolution could be possible. However, the data showed that random evolutionary processes in even the most simple of bacterial proteins actually have impossible hurdles to overcome, even if they only happen one amino acid at a time. The work also demonstrated how key sectors of proteins are so tightly and optimally designed that they tolerate virtually no change whatsoever.

Imagine if this sort of experiment were done in even more complex multicellular biological systems where proteins are considerably larger and more complex. Many types of proteins are only subunits of much larger protein complexes that also have metal ions, carbohydrates, and ribonucleotides integrated into their structures. For example, the shelterin protein complex helps protect and maintain the ends of telomeres. It consists of six different proteins that all provide multiple aspects of cell and genome regulation. These individual proteins are coded by different genes in the genome and must assemble at chromosome endpoints in a specific manner, and they are all dependent on the veracity of each protein subunit. A wide variety of mutations—all associated with some type of genetic disease—have been documented in these proteins.2

Amazingly, some evolutionists think that a large protein would be more favorable to mutation than a smaller one. On the surface, this idea sounds reasonable. However, the idea that having more amino acids could increase the odds of getting a favorable evolutionary outcome through random changes is a false line of logic when applied to engineered systems. Larger and more complex proteins (enzymes, DNA-binding proteins, etc.) clearly represent an incremental or commensurate increase in functional information and ability. They simply have more complex features and perform more complicated functions than smaller proteins. This is particularly true in multicellular organisms where the genome is contained in the nucleus and the cell system is considerably more complex than a bacteria’s cell system.

A good analogy is found in the comparison of a wristwatch and a cell phone. The removal of a single electronic component from each system would result in the failure of the whole system in both devices. The individual components (chips) in each system are more complex in the cell phone than in the wristwatch, but each component is just as critical to the overall system’s function. There is not more room for error in the cell phone just because it is bigger or its components are more numerous.

The concept that larger proteins have more room for error or tolerate more “slop” is a fallacy. Indeed, a recent set of research papers regarding the sequencing of the human exome (protein-coding regions of the genome) showed that variation in human proteins are not only rare, but they are associated with heritable diseases in many of the cases.3 Most of the genetic variation in the human genome is actually associated with non-coding DNA that is involved in controlling the expression of protein-coding genes.

Mutation is also not well-tolerated in proteins because proteins do not act unilaterally. Individual proteins are not isolated components—they are integral parts of a larger cellular system with multiple layers of interlocking genetic and physiological networks.

The main problem regarding false ideas about protein evolution is one of perception associated with the steady diet of academia’s evolutionary false teachings. We see a car, computer, or a toaster and immediately comprehend that it has been designed and engineered by human intelligence. However, when we see biological systems that are magnitudes of complexity more highly designed and engineered than the devices produced by mankind, then we are told that these things “somehow arose by random-chance processes” in some sort of cosmic naturalistic casino. Nothing could be further from the truth, and the data from molecular biology continue to prove it.

Once again, the details of intelligent design clearly displayed in molecular biology—even in a seemingly simple bacterial protein—point directly toward the creative hand of God.